No other region has warmed as much or as rapidly in the past decades as the Arctic. A new project, CACOON, will investigate how coastal Arctic Ocean waters and planktonic communities will respond to changing freshwater inputs driven by on-going climate change. Funded by the British Natural Environment Research Council (NERC) and the German Federal Ministry of Education and Research (BMBF), CACOON will help to better understand and predict changes to the Arctic marine environment. Arctic rivers annually carry around 13% of all dissolved organic carbon transported globally from land to ocean, despite the Arctic Ocean (AO) making up only approximately 1% of the Earth’s ocean volume. Arctic shelf waters are therefore dominated by terrestrial carbon pools and shelf ecosystems intimately linked to freshwater supplies. Arctic ecosystems also contain perennially frozen carbon that may be released by further warming. Climate change already thaws permafrost, reduces sea-ice and increases riverine discharge over much of the pan-Arctic, triggering important feedbacks. The importance of the near-shore region, consisting of several tightly connected ecosystems that include rivers, deltas, estuaries and the continental shelf, is however often overlooked. We need year-round studies to be able to predict the impact of shifting seasonality, fresher water, changing nutrient supply and greater proportions of permafrost-derived carbon on coastal water processes. CACOON addresses this knowledge gap by investigating the near-shore regions of two major Arctic rivers, the Lena and Kolyma, which together drain 19% of the pan-Arctic watershed area. CACOON will quantify the effect of changing freshwater export and terrestrial permafrost thaw on the type and fate of river-borne organic matter (OM) delivered to Arctic coastal waters, and the resultant changes to ecosystem functioning in the coastal AO. We will achieve this though a combined observational, experimental and modelling study. We will conduct laboratory experiments to parameterise the susceptibility of terrigenous carbon to abiotic and biotic transformation and losses, then use the results from these to deliver a marine ecosystem model of the major biogeochemical cycles of carbon, nutrients and OM cycling in these regions.